adds compound definition to glossary

will probably start using it, if not I'll roll back

glossary.md

@@ -5,6 +5,7 @@
 * Sample: what is being produced by a deposition. A sample is made up of different stacked layers of material (target) deposited upon another material (substrate).
 * Target: material "consumed" during the deposition.
 * Substrate: material on which the target is deposited.
+* Compound: which material is a target or a substrate made of; substrates of the same batch are made of the same compound.
 * Layer: one of the layers of material of which a sample is composed; every layer can have different properties, both in the physical sense (i.e. shape, thickness...) and regarding their manufacturing process (i.e. frequency of pulses, deposition temperature and pressure...).
 
 ## eLabFTW glossary
@@ -19,7 +20,7 @@
 * JSON: fancy dictionaries with important data.
 
 ### Endpoints
-Base url: https://{ELAB_BASE_URL}:{PORT}/api/v2
+API URL: `https://{ELAB_BASE_URL}:{PORT}/api/v2`
 
 #### GET, PATCH, DELETE
 * `/items/{elabid}`: data on a resource identified by its elabid.

requirements.txt

@@ -1 +1,2 @@
 requests
+asyncio

src/chained_requests.py

@@ -2,42 +2,79 @@ import os, json, requests
 from getpass import getpass
 from classes import Header
 
-'''
-Starting from the sample's page we'll use this code to pull and return all data from the entries related to the sample and its fabrication.
-'''
+class Layers:
+    def __init__(self, layer_data):
+        try:
+            self.extra = layer_data["metadata_decoded"]["extra_fields"]
+        except KeyError as k:
+            raise KeyError(f"The provided dictionary lacks a \"{k}\" key.")
+        self.target_elabid = self.extra["Target"]["value"]
+        self.start_time = layer_data.get("created_at")
+        self.operator = layer_data.get("fullname")
+        self.description = layer_data.get("body")
+        self.deposition_time = self.extra["Duration"]["value"]
+        self.repetition_rate = self.extra["Repetition rate"]["value"]
+        self.number_of_pulses = float(self.deposition_time) * float(self.repetition_rate)
+        self.temperature = self.extra["Heater temperature "]["value"]
+        self.heating_method = self.extra["Heating Method"]["value"]
 
 class Entrypoint:
     '''
-    Use: Entrypoint(elabid)
+    Entrypoint(sample_data) - where sample_data is a Python dictionary.
 
-    The entrypoint is the starting point of the process of resolving the data chain. The entrypoint must be a sample.
+    The entrypoint is the starting point of the process of resolving the data chain. The entrypoint must be a dictionary containing the data of a sample, created directly from the JSON of the item endpoint on eLabFTW - which can be done through the function get_entry_from_elabid.
+    '''
+    def __init__(self, sample_data):
+        '''
+        Attributes:
+        - self.linked_experiments is a sub-dictionary which only includes links to related experiments.
+        - self.linked_items is a sub-dictionary which only includes links to related items.
+        - self.batch_elabid is an integer (or NoneType if there's an error) containing the elabid of the associated substrate batch entry.
+        '''
+        try:
+            self.extra = sample_data["metadata_decoded"]["extra_fields"]
+        except KeyError as k:
+            raise KeyError(f"The provided dictionary lacks a \"{k}\" key.")
+        self.linked_experiments = sample_data.get("related_experiments_links") or None
+        self.linked_items = sample_data.get("items_links") or None
+        self.batch_elabid = self.extra["Substrate batch"]["value"]
 
-    Currently, the elabid of the sample must be provided. In the future a different method will eventually be implemented.
+
+def get_entry_from_elabid(elabid, entryType="items"):
     '''
-    def __init__(self, elabid):
-        '''
-        Constructor method.
-        self.sample_data is a dictionary of all data on the sample's eLab entry.
-        self.linked_experiments is a sub-dictionary which only includes links to related experiments.
-        self.batch_elabid is an integer (or NoneType if there's an error) containing the elabid of the associated substrate batch entry.
+    Function which returns entrypoint data (as dictionary) from its elabid.
     '''
     header = Header(apikey).dump
-        self.sample_data = requests.get(
+    response = requests.get(
         headers = header,
-            url = f"https://elabftw.fisica.unina.it/api/v2/items/{elabid}",
+        url = f"{ELABFTW_API_URL}/{entryType}/{elabid}",
         verify=True
-        ).json()
-        self.linked_experiments = self.sample_data.get("related_experiments_links") or None
-        try:
-            self.batch_elabid = self.sample_data["metadata_decoded"]["extra_fields"]["Substrate batch"]["value"]
-        except KeyError as k: # if no metadata exists - which means there's a problem with the entry
-            self.batch_elabid = None
+    )
+    if response.status_code // 100 in [2,3]:
+        entry_data = response.json()
+        return entry_data
+    else:
+        raise ConnectionError(f"HTTP request failed with status code: {response.status_code}.")
 
 if __name__=="__main__":
     print("===== DEBUG MODE! =====")
+    ELABFTW_API_URL = "https://elabftw.fisica.unina.it/api/v2"
     apikey = getpass("Paste API key here: ")
+    entryType = None
+    while entryType not in ["items", "experiments"]:
+        eT = input("Enter a valid entry type [items, experiments]: ")
+        match eT:
+            case "items" | "i" | "item":
+                entryType = "items"
+            case "experiments" | "e" | "exp" | "experiment":
+                entryType = "experiments"
+            case _:
+                pass
     elabid = input("Input elabid here [default = 1108]: ") or 1108
-    chain = Entrypoint(elabid)
-    print(json.dumps(chain.sample_data))
-    print(json.dumps(chain.linked_experiments))
-    print(chain.batch_elabid)
+    data = get_entry_from_elabid(elabid, entryType)
+    if entryType == "experiments":
+        layer = Layers(data)
+        print(layer.__dict__)
+    # print(json.dumps(chain.sample_data))
+    # print(json.dumps(chain.linked_experiments))
+    # print(chain.batch_elabid)